A divergent betacoronavirus with a functional furin cleavage site in South American bats

Bats are natural reservoirs for a wide range of RNA viruses. Members of the genus Betacoronavirus, including Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome virus (MERS-CoV), have attracted particular attention due to their recent zoonotic emergence. However, much of the known diversity of betacoronaviruses is based on data from Asia, Africa, and Europe, with limited genomic information available from the Americas. Herein, we report the complete genome of a betacoronavirus identified from a Pteronotus parnellii bat sampled in Brazil. Phylogenetic analysis reveals that this virus is sufficiently distinct from the five recognized Betacoronavirus subgenera to represent a new subgenus. Of note, the spike protein of this bat coronavirus possesses a functional furin cleavage site at the S1/S2 junction with a distinct amino acid sequence motif (RDAR) that differs from that found in SARS-CoV-2 (RRAR) by only one amino acid. Comparative structural analysis identifies other betacoronaviruses in bats with furin cleavage sites at the S1/S2 junction, suggesting that this region is a structurally permissive "hotspot" for cleavage site incorporation. Our study provides a broader understanding of the phylogenetic and functional diversity of bat coronaviruses, offering evolutionary context for features that may be relevant to zoonotic potential.